#!/bin/bash -e

function info() {
echo Usage: `basename $0` 'in.vcf bed'
exit 65
}

while getopts ":p:l:" opts
do
case $opts in
	l) interval=$OPTARG;;
	p) out_prefix=$OPTARG;;
	\?) info;;
esac
done
shift $(($OPTIND - 1))

test $# -lt 2 && info


. $var



echo gatk VariantFiltration
$java_run/gatk37 -R $ref_genome -T VariantFiltration \
-o $out_prefix.filter.vcf --variant $1 -L $2

. $cmd_done